Literature DB >> 26298123

Efficient treatment of induced dipoles.

Andrew C Simmonett1, Frank C Pickard1, Yihan Shao1, Thomas E Cheatham2, Bernard R Brooks1.   

Abstract

Most existing treatments of induced dipoles in polarizable molecular mechanics force field calculations use either the self-consistent variational method, which is solved iteratively, or the "direct" approximation that is non-iterative as a result of neglecting coupling between induced dipoles. The variational method is usually implemented using assumptions that are only strictly valid under tight convergence of the induced dipoles, which can be computationally demanding to enforce. In this work, we discuss the nature of the errors that result from insufficient convergence and suggest a strategy that avoids such problems. Using perturbation theory to reintroduce the mutual coupling into the direct algorithm, we present a computationally efficient method that combines the precision of the direct approach with the accuracy of the variational approach. By analyzing the convergence of this perturbation series, we derive a simple extrapolation formula that delivers a very accurate approximation to the infinite order solution at the cost of only a few iterations. We refer to the new method as extrapolated perturbation theory. Finally, we draw connections to our previously published permanent multipole algorithm to develop an efficient implementation of the electric field and Thole terms and also derive some necessary, but not sufficient, criteria that force field parameters must obey.

Mesh:

Year:  2015        PMID: 26298123      PMCID: PMC4545078          DOI: 10.1063/1.4928530

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  32 in total

1.  A Novel, Computationally Efficient Multipolar Model Employing Distributed Charges for Molecular Dynamics Simulations.

Authors:  Mike Devereux; Shampa Raghunathan; Dmitri G Fedorov; Markus Meuwly
Journal:  J Chem Theory Comput       Date:  2014-09-16       Impact factor: 6.006

2.  Fast evaluation of polarizable forces.

Authors:  Wei Wang; Robert D Skeel
Journal:  J Chem Phys       Date:  2005-10-22       Impact factor: 3.488

3.  Gear formalism of the always stable predictor-corrector method for molecular dynamics of polarizable molecules.

Authors:  Jirí Kolafa
Journal:  J Chem Phys       Date:  2005-04-22       Impact factor: 3.488

Review 4.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

Review 5.  Advanced potential energy surfaces for condensed phase simulation.

Authors:  Omar Demerdash; Eng-Hui Yap; Teresa Head-Gordon
Journal:  Annu Rev Phys Chem       Date:  2013-12-09       Impact factor: 12.703

6.  Fragmentation methods: a route to accurate calculations on large systems.

Authors:  Mark S Gordon; Dmitri G Fedorov; Spencer R Pruitt; Lyudmila V Slipchenko
Journal:  Chem Rev       Date:  2011-08-26       Impact factor: 60.622

7.  Real-space quadrature: a convenient, efficient representation for multipole expansions.

Authors:  David M Rogers
Journal:  J Chem Phys       Date:  2015-02-21       Impact factor: 3.488

8.  Multipolar electrostatics.

Authors:  Salvatore Cardamone; Timothy J Hughes; Paul L A Popelier
Journal:  Phys Chem Chem Phys       Date:  2014-06-14       Impact factor: 3.676

9.  Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.

Authors:  Marie L Laury; Lee-Ping Wang; Vijay S Pande; Teresa Head-Gordon; Jay W Ponder
Journal:  J Phys Chem B       Date:  2015-02-26       Impact factor: 2.991

10.  GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations.

Authors:  Robert E Duke; Oleg N Starovoytov; Jean-Philip Piquemal; G Andrés Cisneros
Journal:  J Chem Theory Comput       Date:  2014-03-03       Impact factor: 6.006

View more
  17 in total

1.  An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Authors:  Jing Huang; Ye Mei; Gerhard König; Andrew C Simmonett; Frank C Pickard; Qin Wu; Lee-Ping Wang; Alexander D MacKerell; Bernard R Brooks; Yihan Shao
Journal:  J Chem Theory Comput       Date:  2017-01-24       Impact factor: 6.006

2.  Isotropic periodic sum for multipole interactions and a vector relation for calculation of the Cartesian multipole tensor.

Authors:  Xiongwu Wu; Frank C Pickard; Bernard R Brooks
Journal:  J Chem Phys       Date:  2016-10-28       Impact factor: 3.488

3.  Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge.

Authors:  Gerhard König; Frank C Pickard; Jing Huang; Andrew C Simmonett; Florentina Tofoleanu; Juyong Lee; Pavlo O Dral; Samarjeet Prasad; Michael Jones; Yihan Shao; Walter Thiel; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2016-08-30       Impact factor: 3.686

4.  Mapping the Drude polarizable force field onto a multipole and induced dipole model.

Authors:  Jing Huang; Andrew C Simmonett; Frank C Pickard; Alexander D MacKerell; Bernard R Brooks
Journal:  J Chem Phys       Date:  2017-10-28       Impact factor: 3.488

5.  Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.

Authors:  Dmitry Bedrov; Jean-Philip Piquemal; Oleg Borodin; Alexander D MacKerell; Benoît Roux; Christian Schröder
Journal:  Chem Rev       Date:  2019-05-29       Impact factor: 60.622

6.  Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Theory Comput       Date:  2016-05-26       Impact factor: 6.006

7.  Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives.

Authors:  Poonam Pandey; Asaminew H Aytenfisu; Alexander D MacKerell; Sairam S Mallajosyula
Journal:  J Chem Theory Comput       Date:  2019-08-29       Impact factor: 6.006

8.  Tinker 8: Software Tools for Molecular Design.

Authors:  Joshua A Rackers; Zhi Wang; Chao Lu; Marie L Laury; Louis Lagardère; Michael J Schnieders; Jean-Philip Piquemal; Pengyu Ren; Jay W Ponder
Journal:  J Chem Theory Comput       Date:  2018-09-19       Impact factor: 6.006

9.  An empirical extrapolation scheme for efficient treatment of induced dipoles.

Authors:  Andrew C Simmonett; Frank C Pickard; Jay W Ponder; Bernard R Brooks
Journal:  J Chem Phys       Date:  2016-10-28       Impact factor: 3.488

Review 10.  An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.

Authors:  Justin A Lemkul; Jing Huang; Benoît Roux; Alexander D MacKerell
Journal:  Chem Rev       Date:  2016-01-27       Impact factor: 60.622

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.